Asymptomatic Carriage and Antimicrobial Resistance of Salmonella in Humans and Poultry in Rural Burkina Faso: Phenotypic and Genotypic Profiles and Associated Risk Factors

Food-borne diseases affect nearly 10% of the global population annually, with <i>Salmonella</i> being a major cause, particularly impacting children, the elderly, and populations in low- and middle-income countries. This study aimed to assess the prevalence, serotype distribution, antibiotic resistance profiles, and genetic determinants of resistance and virulence of <i>Salmonella enterica</i> in humans and poultry in the Nanoro health district. A community-based cross-sectional study involving humans and poultry was conducted in the Nanoro health district. Fresh stool samples (human and poultry cloacal/cecal) were collected, transported under sterile conditions, and processed within two hours using standard bacteriological methods. Phenotypic antibiotic resistance was determined by the Kirby-Bauer disk diffusion method, and whole-genome sequencing (Illumina) identified serotypes, resistance genes, and virulence factors. Logistic regression analyzed associations between <i>Salmonella</i> carriage and host or environmental factors. <i>Salmonella enterica</i> carriage was detected in 8.7% of humans and 7.2% of poultry. Human isolates showed 24% resistance to cephalosporins, while poultry isolates showed 36.8% resistance. Resistance genes, including fosA7, qnrB19, and a cryptic aminoglycoside resistance gene, and virulence genes encoding T3SS-1 and T3SS-2, were detected in both hosts. Logistic regression indicated that residence in Sitaon and Zimidin was associated with ~70% lower odds of carriage (aOR = 0.3), while individuals aged 11-20 and 51-60 years had 2.8-fold higher odds. Carriage was also 60% higher during the rainy season. These findings suggest possible cross-transmission of <i>Salmonella</i> between humans and poultry and the circulation of resistant, potentially virulent strains in the community. Seasonal and age-related variations highlight environmental and behavioral influences on asymptomatic carriage. Integrated One Health surveillance and targeted hygiene interventions are essential to reduce <i>Salmonella</i> transmission and antimicrobial resistance in rural settings.